/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.variant;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackLoader;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.broad.igv.variant.vcf.VCFVariant;
import htsjdk.tribble.Feature;
import org.junit.Assert;
import org.junit.Test;
import java.util.List;
import static junit.framework.Assert.assertEquals;
/**
* User: jacob
* Date: 2012-Aug-29
*/
public class VariantTrackTest extends AbstractHeadlessTest {
@Test
public void testLoadMultiAlleleFreqs() throws Exception {
String filePath = TestUtils.DATA_DIR + "vcf/multi_allele_freqs.vcf";
TestUtils.createIndex(filePath);
Track newTrack = (new TrackLoader()).load(new ResourceLocator(filePath), genome).get(0);
VariantTrack variantTrack = (VariantTrack) newTrack;
List<Feature> featuresList = variantTrack.getFeatures("chr1", 542939 - 10, 543702 + 10);
assertEquals(6, featuresList.size());
double[][] expFreqs = {{0.067}, {0.067}, {0.143, 0.786}, {0.067}, {0.067}, {-1.0}};
assert featuresList.size() == expFreqs.length;
for (int fi = 0; fi < expFreqs.length; fi++) {
double[] expFreq = expFreqs[fi];
double[] actFreq = ((VCFVariant) featuresList.get(fi)).getAlleleFreqs();
Assert.assertArrayEquals(expFreq, actFreq, 1e-12);
}
}
}